swancustomenvironments: Use api for logging

Write to the log file in the api, instead of doing it in the script

SwanCustomEnvironments/swancustomenvironments/scripts/builders/accpy.sh

@@ -10,7 +10,7 @@ fi
 
 # Set up Acc-Py and create the environment
 source "${ACCPY_PATH}/base/${BUILDER_VERSION}/setup.sh"
-acc-py venv ${ENV_PATH} 2>&1 | tee -a ${LOG_FILE}
+acc-py venv ${ENV_PATH} 2>&1
 
 # Activate the environment
 _log "Setting up the environment..."
@@ -19,13 +19,13 @@ eval "${ACTIVATE_ENV_CMD}"
 
 # Install packages in the environment and the same ipykernel that the Jupyter server uses
 _log "Installing packages from ${REQ_PATH}..."
-pip install -r "${REQ_PATH}" "ipykernel==${IPYKERNEL_VERSION}" ${NXCALS} ${SPARKMONITOR} ${SPARKCONNECTOR_DEPENDENCIES} 2>&1 | tee -a ${LOG_FILE} # TODO
+pip install -r "${REQ_PATH}" "ipykernel==${IPYKERNEL_VERSION}" ${NXCALS} ${SPARKMONITOR} ${SPARKCONNECTOR_DEPENDENCIES} 2>&1 # TODO
 
 
 # -------------- HACK SECTION --------------
 # Install SPARKCONNECTOR_DEPENDENCIES separately, install SparkConnector without its dependencies and change the configuration file
 # TODO: Remove this when the SparkConnector package gets properly updated
 if [ -n "${INSTALL_NXCALS}" ]; then
-    pip install ${SPARKCONNECTOR} --no-deps 2>&1 | tee -a ${LOG_FILE}
-    wget https://raw.githubusercontent.com/swan-cern/jupyter-extensions/refs/heads/swan-on-tn/SparkConnector/sparkconnector/configuration.py -O ${ENV_PATH}/lib/python3.11/site-packages/sparkconnector/configuration.py 2>&1 | tee -a ${LOG_FILE}
+    pip install ${SPARKCONNECTOR} --no-deps 2>&1
+    wget https://raw.githubusercontent.com/swan-cern/jupyter-extensions/refs/heads/swan-on-tn/SparkConnector/sparkconnector/configuration.py -O ${ENV_PATH}/lib/python3.11/site-packages/sparkconnector/configuration.py 2>&1
 fi

SwanCustomEnvironments/swancustomenvironments/scripts/builders/mamba.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 # Create the environment, install packages and the same ipykernel that the Jupyter server uses
-mamba create -p ${ENV_PATH} --file ${REQ_PATH} "ipykernel==${IPYKERNEL_VERSION}" -y | tee -a ${LOG_FILE}
+mamba create -p ${ENV_PATH} --file ${REQ_PATH} "ipykernel==${IPYKERNEL_VERSION}" -y
 
 # Activate the environment
 _log "Setting up the environment..."

SwanCustomEnvironments/swancustomenvironments/scripts/builders/venv.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 # Create the environment
-python3 -m venv ${ENV_PATH} 2>&1 | tee -a ${LOG_FILE}
+python3 -m venv ${ENV_PATH} 2>&1
 
 # Activate the environment
 _log "Setting up the environment..."
@@ -10,4 +10,4 @@ eval "${ACTIVATE_ENV_CMD}"
 
 # Install packages in the environment and the same ipykernel that the Jupyter server uses
 _log "Installing packages from ${REQ_PATH}..."
-pip install -r "${REQ_PATH}" "ipykernel==${IPYKERNEL_VERSION}" 2>&1 | tee -a ${LOG_FILE}
+pip install -r "${REQ_PATH}" "ipykernel==${IPYKERNEL_VERSION}" 2>&1

SwanCustomEnvironments/swancustomenvironments/scripts/makenv.sh

@@ -14,12 +14,11 @@ if [ -n "${CURRENT_ENV_NAME}" ]; then
     exit 1
 fi
 
-LOG_FILE=/tmp/makenv.log # File to keep a backlog of this script output
 GIT_HOME="$HOME/SWAN_projects" # Path where git repositories are stored
 
 _log () {
     if [ "$*" == "ERROR:"* ] || [ "$*" == "WARNING:"* ] || [ "${JUPYTER_DOCKER_STACKS_QUIET}" == "" ]; then
-        echo "$@" 2>&1 | tee -a ${LOG_FILE}
+        echo "$@" 2>&1
     fi
 }
 
@@ -144,7 +143,7 @@ if [[ "$REPOSITORY" =~ $REPO_GIT_PATTERN ]]; then
     # Otherwise, use the existing one in the SWAN_projects folder
     if [ ! -d "${GIT_REPO_PATH}" ]; then
         _log "Cloning the repository from ${REPOSITORY}..."
-        git clone $REPOSITORY -q "${TMP_REPO_PATH}" 2>&1 | tee -a ${LOG_FILE}
+        git clone $REPOSITORY -q "${TMP_REPO_PATH}" 2>&1
         if [ $? -ne 0 ]; then
             _log "ERROR: Failed to clone Git repository" && exit 1
         fi
@@ -174,12 +173,12 @@ HOME=/home/$USER source "${BUILDER_PATH}"
 
 # Install environment kernel.
 # Setting JUPYTER_PATH prevents ipykernel installation from complaining about non-found kernelspec
-JUPYTER_PATH=${ENV_PATH}/share/jupyter python -m ipykernel install --name "${ENV_NAME}" --display-name "Python (${ENV_NAME})" --prefix "${ENV_PATH}" 2>&1 | tee -a ${LOG_FILE}
+JUPYTER_PATH=${ENV_PATH}/share/jupyter python -m ipykernel install --name "${ENV_NAME}" --display-name "Python (${ENV_NAME})" --prefix "${ENV_PATH}" 2>&1
 
 # Make sure the Jupyter server finds the new environment kernel in /home/$USER/.local
 # We modify the already existing Python3 kernel with the kernel.json of the environment
 KERNEL_JSON=${ENV_PATH}/share/jupyter/kernels/${ENV_NAME}/kernel.json
-ln -f -s ${KERNEL_JSON} /home/$USER/.local/share/jupyter/kernels/python3/kernel.json | tee -a ${LOG_FILE}
+ln -f -s ${KERNEL_JSON} /home/$USER/.local/share/jupyter/kernels/python3/kernel.json
 
 # For NXCALS, configure the environment kernel and terminal with some variables to
 # ensure the connection with the cluster works properly.
@@ -202,7 +201,7 @@ if [ -n "${INSTALL_NXCALS}" ]; then
     --arg SPARK_DRIVER_EXTRA_JAVA_OPTIONS "${SPARK_DRIVER_EXTRA_JAVA_OPTIONS}" \
     '. + {env: {$SPARK_HOME, $PYSPARK_PYTHON, $PATH, $VIRTUAL_ENV, $SPARK_DRIVER_EXTRA_JAVA_OPTIONS}}' \
     ${KERNEL_JSON} > ${NEW_KERNEL}
-    mv -f ${NEW_KERNEL} ${KERNEL_JSON} 2>&1 | tee -a ${LOG_FILE}
+    mv -f ${NEW_KERNEL} ${KERNEL_JSON} 2>&1
 
     # Terminal configuration
     # Only SPARK_HOME and PYSPARK_PYTHON are needed, since PATH and VIRTUAL_ENV are already

SwanCustomEnvironments/swancustomenvironments/serverextension.py

@@ -13,6 +13,9 @@ class SwanCustomEnvironmentsApiHandler(APIHandler):
     # Path to the script used to create custom environments
     makenv_path = path.join(path.dirname(__file__), "scripts/makenv.sh")
 
+    # Path to the file where the log of the makenv.sh script is written
+    LOG_FILE = "/tmp/makenv.log"
+
     @web.authenticated
     def get(self):
         """
@@ -37,9 +40,12 @@ def get(self):
 
         makenv_process = subprocess.Popen([self.makenv_path, *arguments], stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
 
-        for line in iter(makenv_process.stdout.readline, b""):
-            self.write(line.decode('utf-8'))
-            self.flush()
+        with open(self.LOG_FILE, "w") as log_file:
+            for line in iter(makenv_process.stdout.readline, b""):
+                line = line.decode('utf-8')
+                log_file.write(line) # send log to file (for debugging)
+                self.write(line) # send log to frontend
+                self.flush()
 
         self.finish()